Cancer is a primary cause of mortality, accounting for 1 in 4 of all deaths. The treatment of cancer has traditionally been based on the law of averages—what works best for the largest number of patients. However, owing to the molecular heterogeneity in cancer, often less than 25% of treated individuals profit from the approved therapies. Individualized medicine based on tailored treatment of patients is regarded as a potential solution to low efficacies and high costs for innovation in drug development.
Antigen specific immunotherapy aims to enhance or induce specific immune responses in patients and has been successfully used to control cancer diseases. T cells play a central role in cell-mediated immunity in humans and animals. The recognition and binding of a particular antigen is mediated by the T cell receptors (TCRs) expressed on the surface of T cells. The T cell receptor (TCR) of a T cell is able to interact with immunogenic peptides (epitopes) bound to major histocompatibility complex (MHC) molecules and presented on the surface of target cells. Specific binding of the TCR triggers a signal cascade inside the T cell leading to proliferation and differentiation into a maturated effector T cell.
The identification of a growing number of pathogen- and tumor-associated antigens (TAA) led to a broad collection of suitable targets for immunotherapy. Cells presenting immunogenic peptides (epitopes) derived from these antigens can be specifically targeted by either active or passive immunization strategies. Active immunization may tend to induce and expand antigen specific T cells in the patient, which are able to specifically recognize and kill diseased cells. Different antigen formats can be used for tumor vaccination including whole cancer cells, proteins, peptides or immunizing vectors such as RNA, DNA or viral vectors that can be applied either directly in vivo or in vitro by pulsing of DCs following transfer into the patient.
Cancers may arise from the accumulation of genomic mutations and epigenetic changes, of which a fraction may have a causative role. In addition to tumor associated antigens, human cancers carry on average 100-120 non-synonymous mutations, of which many are targetable by vaccines. More than 95% of mutations in a tumor are unique and patient specific (Weide et al. 2008: J. Immunother. 31, 180-188). The number of protein changing somatic mutations, which may result in tumor specific T cell epitopes, is in the range of 30 to 400. It has been predicted in silico that there are 40 to 60 HLA class I restricted epitopes per patient derived from tumor specific somatic mutations (Azuma et al. 1993: Nature 366, 76-79). Moreover, de novo immunogenic HLA class II restricted epitopes likely also result from tumor-associated mutations, however their number is still unknown.
Notably, some non-synonymous mutations are causally involved in neoplastic transformation, crucial for maintaining the oncogenic phenotype (driver mutations) and may represent a potential “Achilles' heel” of cancer cells. Mutations found in the primary tumor may also be present in metastases. However, several studies demonstrated that metastatic tumors of a patient acquire additional genetic mutations during individual tumor evolution which are often clinically relevant (Suzuki et al. 2007: Mol. Oncol. 1 (2), 172-180; Campbell et al. 2010: Nature 467 (7319), 1109-1113). Furthermore, also the molecular characteristics of many metastases deviate significantly from those of primary tumors.
Tumor heterogeneity is perceived as major hurdle for the efficacy of currently available therapies. The technical problem underlying the present invention is to provide a highly effective cancer vaccination strategy that overcomes the hurdles of existing approaches relating to tumor heterogeneity.
The present invention relates to a personalized therapy concept that integrates personal disease genetics to create customized therapies in oncology. Human cancers express various immunogenic shared tumor antigens and carry dozens to hundreds of non-synonymous mutations, of which many are targetable by T cells. As they are not subject to central immune tolerance, these mutations are ideal candidates for vaccine development. The present invention makes use of personalized vaccines, in particular RNA vaccines, targeting individual expression patterns of tumor antigens and individual tumor mutations. The present concept exploits genetic tumor alterations for the sake of patients instead of being hampered by them.
Instead of searching for a common molecular denominator in many patients for targeting, the present invention exploits the antigenic target repertoire of each single individual patient. Instead of accepting trade-offs by providing a treatment that is designed for the average, the present invention provides the best combination for each individual patient. This is not only a paradigm shift, but opens up new opportunities to solve critical problems in current cancer drug development such as broad inter-individual variability and intra-tumor clonal heterogeneity. The present invention allows an optimal exploitation of the antigen repertoire in patients.
Specifically, the present application relates to a poly-specific targeting of the whole individual tumor antigen repertoire found in each individual cancer patient, including both non-mutated and mutated tumor antigens. For targeting of non-mutated tumor antigens, a tumor antigen target portfolio (warehouse) covering a large fraction of the patients can be used. This warehouse is a drug repository for “off the shelf” pre-manufactured vaccines and combining them with a vaccination cocktail for use in an individual patient. Together with mutanome engineered vaccines, this allows an optimal exploitation of the antigen repertoire in patients.
The present invention involves the identification of patient specific cancer mutations and targeting a patient's individual cancer mutation “signature”. The identification of non-synonymous point mutations resulting in amino acid changes that will be presented the patient's major histocompatibility complex (MHC) molecules provides novel epitopes (neo-epitopes) which are specific for the patient's cancer but are not found in normal cells of the patient. Collecting a set of mutations from cancer cells such as circulating tumor cells (CTC) allows the provision of a vaccine which induces an immune response potentially targeting the primary tumor even if containing genetically distinct subpopulations as well as tumor metastases. For vaccination, such neo-epitopes identified according to the present application are preferably provided in a patient in the form of a polypeptide comprising said neo-epitopes and following appropriate processing and presentation by MHC molecules the neo-epitopes are displayed to the patient's immune system for stimulation of appropriate T cells.
Preferably, according to the invention, immune responses are induced in the patient by administering RNA encoding an immunogenic gene product, e.g. a peptide or polypeptide, comprising one or more immunogenic epitopes against which an immune response is to be induced. Such immunogenic gene product may comprise the entire tumor antigen against which an immune response is to be induced or it may comprise a portion thereof such as a T cell epitope. A strategy wherein in vitro transcribed RNA (IVT-RNA) is directly injected into a patient by different immunization routes has been successfully tested in various animal models. RNA may be translated in transfected cells and the expression product following processing presented on the MHC molecules on the surface of the cells to elicit an immune response.
The advantages of using RNA as a kind of reversible gene therapy include transient expression and a non-transforming character. RNA does not need to enter the nucleus in order to be expressed and moreover cannot integrate into the host genome, thereby eliminating the risk of oncogenesis. Transfection rates attainable with RNA are relatively high. Furthermore, the amounts of protein achieved correspond to those in physiological expression.